comparePWMFreqs: Compare the matches to a set of PWMs in two sets of sequences

In steveped/motifMatching: Functions used for matching motifs in DNA/RNA Strings

Description

Compare the frequency of matches to a set of motifs within two sets of sequences

Usage

comparePWMFreqs(refSeq, testSeq, motifs, minScore = "90%",
  testCounts = NULL, useFisher = FALSE)

Arguments

refSeq	the set of reference sequences as an XStringSet
testSeq	the set of test sequences as an XStringSet
motifs	the set of motifs as a MotifList
minScore	the minimum matching score for the PWM
testCounts	if resampling over multiple reference sequences, supply this as the output from countViews
useFisher	logical. Adds the p-values from the fisher.test function to the output

Details

Used to compare matches to the same set of motifs within two sets of sequences.

If using to bootstrap multiple sets of reference sequences, set useFisher = FALSE and use lapply (or it's relatives) to specify multiple sets of XStringSets.

If simply testing two sets of sequences, set iseFisher = TRUE to add p-values from Fisher tests to every motif

Value

Returns a tbl_df with columns motif, testFreq, refFreq & oddsRatio, with the additional column p if useFisher=TRUE. If the argument useFisher=TRUE, the odds ratio will be the conditional MLE estimate as calculated using that function, whereas otherwise it will be the sample odds ratio.

Author(s)

Steve Pederson

See Also

tbl_df

steveped/motifMatching documentation built on May 30, 2019, 5:39 p.m.